On 3/14/19 3:21 PM, Phuong Chau wrote:
Hello everyone, I want to generate gromacs topology of a substance (a single chemical) which has a pdb file generated by RDKIT from SMILES representation of that substance (MolToPDBFile). However, when I input the pdb file generated by RDKit, it showed the error of "Residue 'UNL' not found in residue topology database". The general idea is: Input: Name of a substance (single chemical) Output: pdb file of the substance (does not have to be generated by RDKit) and the topology file of its susbtance that is generated by Gromacs. Could anyone tell me any possible solution to solve this problem?
pdb2gmx isn't magic :) http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
